# Some Rcmdr menus for the BiclustGUI package
# When the plug-in is loaded, these menus are merged with the standard Rcmdr menus



#type   menu/item      		operation/parent  	label                              	command/menu    		activation    		install?

### DEFINE TOP BICLUSTERING MENU				
menu	BICLUSTERINGmenu       	topMenu	  		""					"" 				""			""
item 	topMenu	         	cascade	  		"Biclustering"                        	BICLUSTERINGmenu      		""            		""


### Search 
item 	BICLUSTERINGmenu	command			"Search Method..."			"search_WINDOW"			""			""
item 	BICLUSTERINGmenu	separator		""					""				""			""



### BiClust Package Menu	
menu	biclustmenu	   	BICLUSTERINGmenu   	""             				""				""			""
item	BICLUSTERINGmenu   	cascade	   		"Biclust"				biclustmenu			""			""


item	biclustmenu	   	command			"Biclustering - Plaid"			"biclustplaid_WIN"  		"activeDataSetP()"	""
item	biclustmenu	   	command			"Biclustering - CC" 			"biclustCC_WIN"     		"activeDataSetP()"	""
item	biclustmenu	   	command			"Biclustering - XMotif"			"biclustXMotif_WIN" 		"activeDataSetP()"	""
item	biclustmenu	   	command			"Biclustering - Spectral"		"biclustspectral_WIN" 		"activeDataSetP()"	""
item	biclustmenu	   	command			"Biclustering - QuestMotif"		"biclustquest_WIN"		"activeDataSetP()"	""
item	biclustmenu	   	command			"Biclustering - Bimax"			"biclustbimax_WIN"		"activeDataSetP()"	""



### Fabia Package Menu	
menu	fabiamenu		BICLUSTERINGmenu	""					""				""			""
item	BICLUSTERINGmenu	cascade			"Fabia"					fabiamenu			""			""


item	fabiamenu		command			"Fabia - Laplace Prior"			"fabialaplace_WIN"		"activeDataSetP()"	""
item	fabiamenu		command			"Fabia - Post-Projection"		"fabiapostprojection_WIN"	"activeDataSetP()"	""
item	fabiamenu		command			"Fabia - Sparseness Projection"		"fabiasparsenessprojection_WIN"	"activeDataSetP()"	""
item	fabiamenu		command			"Fabia - SPARSE"			"fabiaSPARSE_WIN"		"activeDataSetP()"	""

### s4vd Package Menu
menu	s4vdmenu		BICLUSTERINGmenu	""					""				""			""
item	BICLUSTERINGmenu	cascade			"s4vd"					s4vdmenu			""			""

item	s4vdmenu		command			"Sparse Singular Value Decomposition"	"ssvd_WIN"			"activeDataSetP()"	""
item	s4vdmenu		command			"SSVD with Stability Selection (s4vd)"	"s4vd_WIN"			"activeDataSetP()"	""

### BiBitR Package Menu
menu  bibitmenu BICLUSTERINGmenu  ""          ""          ""      ""
item  BICLUSTERINGmenu  cascade   "BiBitR"          bibitmenu     ""      ""

item bibitmenu    command   "BiBit with Noise Allowance"            "bibit_WIN"     "activeDataSetP()"  ""
item bibitmenu    command   "BiBit with Provided Pattern"           "bibit3_WIN"    "activeDataSetP()"  ""



### ISA Package Menu
item	BICLUSTERINGmenu	command			"ISA"					"isadefault_WIN_TEMPORARY"		"activeDataSetP()"	""

### iBBiG Package Menu
item	BICLUSTERINGmenu	command			"iBBiG"					"iBBiG_WIN"			"activeDataSetP()"	""

### rqubic Package Menu
item	BICLUSTERINGmenu	command			"rqubic"				"rqubic_WINDOW"			""			""

## BicARE Package Menu
item	BICLUSTERINGmenu	command			"BicARE"				"bicare_WINDOW"			""			""

### DEFINE TOP BICLUSTERING HELP & EXPORT MENU		
menu	BICLUSTERINGHELPmenu  	topMenu	  		""					"" 				""			""
item 	topMenu	          	cascade	  		"Biclustering - Help & Utilities"     	BICLUSTERINGHELPmenu      	""               	""

## Set Plot Grid Menu
item 	BICLUSTERINGHELPmenu	command			"Set Plot Grid"				"plotgridpref_WINDOW"		""			""			
item 	BICLUSTERINGHELPmenu	separator		""					""				""			""

## Clear Results Menu
item	BICLUSTERINGHELPmenu	command			"Clear All Results..."			"clearresults_WINDOW"		""			""


## Export Menu
menu	exportmenu		BICLUSTERINGHELPmenu	""					""				""			""
item	BICLUSTERINGHELPmenu	cascade			"Export Results ..."			exportmenu			""			""


item 	exportmenu		command			"as Text-file"				"exportTXT_WINDOW"		""			""
item 	exportmenu		command			"for Furby"				"exportFURBY_WINDOW"		""			""


## Extract/Find Menu		
menu	extractfindmenu		BICLUSTERINGHELPmenu	""					""				""			""
item	BICLUSTERINGHELPmenu	cascade			"Extract/Find Biclusters..."		extractfindmenu			""			""

item	extractfindmenu		command			"Extract Biclusters"			"extractbicluster_WINDOW"	""			""
item	extractfindmenu		command			"Find Biclusters"			"findbiclusters_WINDOW"		""			""
item  extractfindmenu   command     "Maximal Biclusters"  "MaxBC_WINDOW"            ""      ""


## Help Menu	
menu	helpmenu		BICLUSTERINGHELPmenu	""					""				""			""
item	BICLUSTERINGHELPmenu	cascade			"Help Documentation"			helpmenu			""			""

item	helpmenu		command			"BiclustGUI Website..."			"biclustguiwebsitelink" ""			""
item 	helpmenu		command			"Helppage BiclustGUI..."		"biclustGUI_help"		""			""
item 	helpmenu		command			"Vignette BiclustGUI..."		"openGUIVignette"		""			""
item 	helpmenu		command			"Template Scripts"			"openGUIScripts"		""			""

## Shiny Menu
menu 	shinymenu		BICLUSTERINGHELPmenu	""					""				""			""
item 	BICLUSTERINGHELPmenu	cascade			"BiclustGUI Shiny App"			shinymenu			""			""

item	shinymenu		command			"Online Version"				"shinylinkwebsite"			""			""
item	shinymenu		command			"Download Stand-Alone Version"	"shinylinkstandalone"		""			""


## Save/Load Menu
item BICLUSTERINGHELPmenu	command			"Save/Load"				"saveload_WINDOW"		""			""

## Draw Heatmap Menu	
item BICLUSTERINGHELPmenu	command			"Draw Heatmaps"				"image_WINDOW"			""			""

## Jaccard Index Menu
item BICLUSTERINGHELPmenu	command			"Jaccard Index..."			"jaccard_WINDOW"		""			""

## Jaccard Heatmap
item BICLUSTERINGHELPmenu	command			"Jaccard Index Heatmap"			"heatmapJI_WINDOW"		""			""

